title: CRBT50 [NB_cont_41]


title: 7754315097_J: 14836-DAY1

status: Public on Nov 25 2019

type: RNA

city: Budapest

first: Gábor

middle: Nándor

last: Than

address: Magyar tudósok krt. 2

department: Institute of Enzymology

country: Hungary

institute: Research Centre for Natural Sciences

description: replicate 2, day 1

hyb_protocol: Labeled cRNAs were hybridized to HumanHT-12v4 Expression BeadChips.

scan_protocol: BeadChips were imaged using an Illumina BeadArray Reader, and raw data were obtained with Illumina BeadStudio Software V.3.4.0.

data_processing: Expression intensities were background-corrected using the default method in the lumiR function of the LUMI package. Data was variance stabilized via log2 transformation and normalized with the quantile method. From the 47,307 probes on the array, we included those 25,025 probes (14,197 unique genes) into the further steps of analysis which had at least two samples with a False Discovery Rate (FDR)-adjusted p-value of <0.1.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: villous trophoblast culture, replicate 2, day 1

label_protocol: DNase-treated RNA samples (n=24; 500ng) were amplified and biotin-labeled with the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Placentas were taken from normal pregnant women delivering at term. Primary villous trophoblasts were isolated and plated on collagen-coated 12-well plates at 3x1,000,000 cells/well density in Iscove’s modified Dulbecco’s medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: Total RNA was isolated from primary trophoblasts harvested on Days 0-7 of differentiation with RNeasy kit.

treatment_protocol: The effect of trophoblast differentiation on gene expression was tested by keeping primary trophoblasts in IMDM containing 5% non-pregnant human serum and 1% P/S for 7 days. The medium was replenished every 24h, and cells were harvested for total RNA in every 24h.

tag: cell type

value: villous trophoblast

tag: differentiation day


title: 7754315097_K: 14836-DAY2

description: replicate 2, day 2

source_name: villous trophoblast culture, replicate 2, day 2


title: 7754315097_I: 14836-DAY0

description: replicate 2, day 0

source_name: villous trophoblast culture, replicate 2, day 0


title: 7754315097_H: 14685-DAY7

description: replicate 1, day 7

source_name: villous trophoblast culture, replicate 1, day 7


title: 7754315097_G: 14685-DAY6

description: replicate 1, day 6

source_name: villous trophoblast culture, replicate 1, day 6


title: CRBT45 [NB_cont_36]

type: SRA

city: Lyon

first: Mathilde

last: PARIS

address: 32-34 avenue Tony Garnier

department: Institut de Genomique Fonctionnelle de Lyon

country: France

institute: CNRS

description:
processed data file:
est_counts_155cells_CellsRenamed_GeneNames.txt
description_155cells.txt

library_source: transcriptomic

data_processing:
Reads were processed using Kallisto (Bray et al. Nature Biotechnology 2016) and the mouse genome (ENSEMBL Release GRCm38) with the following parameters : -l 350 -s 50 -b 100.
Gene levels were obtained by summing up TPM or counts over their transcripts.
We selected 155 cells for which at least 20% of the sequenced reads mapped to the annotation, for a total of at least 50000 mapped reads.
We selected 3422 genes that had a raw read count above 10 in at least 5 selected cells.
Gene counts were TMM normalized using the function normalizeBetweenArrays from the R package limma, so that the quantiles of the different samples were identical.
Genome_build: GRCm38)
Supplementary_files_format_and_content: est_counts_155cells_CellsRenamed_GeneNames.txt : tab-delimited text file containing estimted counts for each gene (rows) in each Sample (columns). The names of the genes and cells are given.
Supplementary_files_format_and_content: description_155cells.txt: tab-delimited text file decribing each cell (e.g. cell type)

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Single-cell suspensions, previously stained with the Fixable Viability Dye eFluor780 (Thermofisher 65-0865-14), were sorted on a 4-laser BD FACS Influx (BD Biosciences) equipped with a 100 µm nozzle. Single live cells were gated based on forward scatter, side scatter, trigger pulse width, and viability dye parameters. Autofluorescent cells were excluded based on their non-specific signal in the Amcyan channel. Cells were further gated as Gad67-GFP+, Olig2-Tomato+, or double positive. Single cells were FACS sorted into 96-well PCR plates containing 3μL lysis buffer (10:1 mix of Resuspension Buffer and Lysis Enhancer from Cells Direct one-step qRT-PCR kit, Thermofisher 11753100)
SMART-Seq2 according to Picelli et al. (2014)

treatment_protocol: NBL, OligNBL and OL single cells were dissociated from dissected SVZ and CC from demyelinated mice (8-10 weeks old, n=5 mice) 6 days after LPC injection, during the peak of cell mobilization in the SVZ. Control NB and O single cells were collected from healthy non-injected mice (8-10 weeks old, n=5 mice)

tag: strain

tag: age

value: 8-10 weeks old

tag: tissue

value: brain (sub-ventricular zone and corpus callosum)

tag: lesion state

value: control

value: NB

tag: cell population name


title: 7754315097_F: 14685-DAY5

description: replicate 1, day 5

source_name: villous trophoblast culture, replicate 1, day 5


title: CRBT47 [NB_cont_38]


title: 2mo-WT-9F

city: Cambridge

first: Stefka

last: Gyoneva

state: MA

address: 225 Binney St.

country: USA

institute: Biogen, Inc

data_processing:
Raw reads were aligned to mouse genome build mm10 using STAR version 2.5.2a and transcripts quantified with RSEM version 1.2.26
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text; gene level count table - *_genes.estcount_table.txt; gene level FPKM table - *_genes.fpkm_table.txt; gene level TPM table - *_genes.tpm_table.txt

source_name: Microglia

growth_protocol: All mice used in the current manuscript are littermate controls derived from Cx3cr1+/eGFP crosses. The mice were maintained on a normal diet in a 12-hour light/dark cycle. Approximately five mice were used per group (per sex, age, genotype and treatment).

extract_protocol:
Brains were finely minced with a razor blade and tissues were dissociated to single cell suspension with Accutase on ice for 30 min. Cell suspensins were resuspended with 33% Percoll and centrifuged for 15 min at 800g (no brake). Cells were washed, stained and subjected to sorting for CD11b(+)CD45(lo) cells. RNA was isolated from sorted microglia using Qiagen Universal AllPrep kit (Qiagen 80004) according to the manufacturer’s instructions.
cDNA for RNA-Seq libraries was prepared using 10 ng of RNA using the SmartSeq v4 Ultra Low RNA Input Library prep protocol (Clontech 634889) according to the manufacturer’s instruction.
The cDNA (250 ng starting material) was then tagged and fragmented with the NexteraXT DNA Library Preparation kit (Illumina FC-131-1024) according to the manufacturer’s instructions. Quality of amplified cDNA and fragmented libraries was assessed on a Bioanalyzer with the High Sensitivity DNA chips (Agilent 5067-4627). Tagged libraries were pooled (8 nM total DNA) and sequenced on an Illumina HiSeq2500 sequencer, with target depth of 20 million of 50 bp paired end reads

treatment_protocol: Mice were deeply anesthetized with 10 mg/kg ketamine, 30 mg/kg xylazine until they failed to respond to toe pinch and transcardially perfused with cold phosphate-buffered saline (PBS). Mice for the LPS study were euthanized by CO2 asphyxiation, peritoneal cells were isolated by flushing the peritoneal cavity with cold PBS, and then perfused. In all cases, the brain was then isolated and stored in PBS on ice until processing.

tag: cx3cr1 genotype

value: WT

value: 2 months

tag: Sex

value: F

value: Microglia

tag: treatment

value: None/naïve


title: CRBT44 [NB_cont_35]


title: 7754315097_E: 14685-DAY4

description: replicate 1, day 4

source_name: villous trophoblast culture, replicate 1, day 4


title: 7754315097_L: 14836-DAY3

description: replicate 2, day 3

source_name: villous trophoblast culture, replicate 2, day 3


title: 2mo-WT-7F


title: 901379: HDM - mIL13Ra2-Fc

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include read count for each sample

source_name: lung

extract_protocol:
Total RNA was purified using MagMAX™-96 Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen).
Strand-specific RNA-seq libraries were prepared using KAPA stranded mRNA-Seq Kit (KAPA Biosystems).

value: lung

value: HDM

tag: antibody

tag: genotype

value: Il4hu/hu Il4rahu/hu


title: CRBT43 [NB_cont_34]


title: 7754315097_D: 14685-DAY3

description: replicate 1, day 3

source_name: villous trophoblast culture, replicate 1, day 3


title: 901378: HDM - mIL13Ra2-Fc


title: 2mo-WT-6F


title: CRBT41 [NB_cont_32]


title: 901377: HDM - mIL13Ra2-Fc


title: 901375: HDM - mIL13Ra2-Fc


title: 901376: HDM - mIL13Ra2-Fc


title: CRBT42 [NB_cont_33]


title: 901373: HDM - mIL13Ra2-Fc


title: 7754315097_C: 14685-DAY2

description: replicate 1, day 2

source_name: villous trophoblast culture, replicate 1, day 2


title: 7754315097_B: 14685-DAY1

description: replicate 1, day 1

source_name: villous trophoblast culture, replicate 1, day 1


title: 901372: HDM – control mIgG

value: control mIgG


title: 2mo-WT-4M

value: M


title: CRBT39 [NB_cont_30]


title: 901371: HDM – control mIgG


title: 2mo-WT-8F


title: 2mo-WT-3M


title: 901370: HDM – control mIgG


title: CRBT38 [NB_cont_29]


title: 901369: HDM – control mIgG


title: 7911747040_E: 15010-DAY0

description: replicate 3, day 0

source_name: villous trophoblast culture, replicate 3, day 0


title: 2mo-WT-2M


title: 901368: HDM – control mIgG


title: CRBT37 [NB_cont_28]


title: 2mo-WT-1M


title: 901365: HDM - IL4 Ab

value: IL4 Ab


title: 901364: HDM - IL4 Ab


title: 901366: HDM – control mIgG


title: CRBT40 [NB_cont_31]


title: 901374: HDM - mIL13Ra2-Fc


title: YS

city: St. Louis

first: Kyunghee

last: Choi

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis, School of Medicine

data_processing:
cellranger2.0.1 pipeline (10x genomics)
Genome_build: mm10
Supplementary_files_format_and_content: mtx files of gene vs cell expression matices; tsv files for barcodes and genes

source_name: yolk sac

growth_protocol: Not applicable.

extract_protocol:
Single cell suspension at 300 cells/uL in PBS were subjected to the Chromium 10X Genomics library construction and HiSeq2500 sequencing (The Genome Technology Access Center, Washington University in St. Louis).
single cell RNA-seq

treatment_protocol: Yolk sacs were dissected from equal numbers of mouse E9.5 and E10.5 embryos, mixed together and dissociated with 0.25% collagenase at 37°C for 30 minutes. The cells were stored at -80°C in fetal bovine serum with 10% DMSO. When the 10x genomics instrument was ready, the cells were thawed and washed, and stained using antibody against Ter119 (eBioscience). Dead cells and ~70% of Ter119+ cells were excluded by sorting to enrich live non-erythroid cells. The single cell suspension was washed with and re-suspended in PBS.

value: mouse embryo

tag: development stage

value: yolk sac of E9.5 and E10.5 mouse embryos

value: extraembryonic tissue


title: 901367: HDM – control mIgG


title: CRBT36 [NB_cont_27]

value: 8-10 weeks old

value: brain (sub-ventricular zone and corpus callosum)


title: 7754315097_A: 14685-DAY0

description: replicate 1, day 0

source_name: villous trophoblast culture, replicate 1, day 0

value: villous trophoblast


title: 901363: HDM - IL4 Ab


title: EB

source_name: embyoid body differentiation

growth_protocol: Mouse ES cells were maintained and for EB differentiation in serum as previously reported. Briefly, ES cells were maintained on mouse embryo fibroblast (MEF) feeder cell layers in Dulbecco-modified Eagle medium containing 15% fetal bovine serum, 100 units/mL LIF, 1× MEM Non-Essential Amino Acids Solution (Gibco), 1× GlutamaxTM Supplement (Gibco), and 4.5 × 10–4 M 1-Thioglycerol (MTG, Sigma). For feeder-free culture, ES cells were maintained in gelatin-coated dish in Iscove’s modified Dulbecco medium (IMDM) with the same supplements as used for maintenance on feeder. For EB differentiation, ES cells were first transferred into feeder-free condition for 2 days, then single-cell suspensions were prepared, and 8,000 cells were added per mL to a differentiation medium of IMDM containing 15% differentiation-screened fetal calf serum, 1× Glutamax, 50 μg/mL ascorbic acid, and 4.5 × 10–4 M MTG on a bacteriological Petri dish.

treatment_protocol: Day 4 EBs were dissociated with Accutase solution (Sigma) for 5 minutes into single cells. The single cell suspension of both samples was washed with and re-suspended in standard cell-freezing buffer (10% DMSO and 90% FBS) and kept in freezing box to cooled down to -80°C. The frozen samples were kept at  -80°C. For scRNA-seq analysis, samples were thawed into PBS plus 15% FBS and sorted using FACS for live cells. Sorted cells were re-suspended in PBS and ready for scRNA-seq assay.

value: ES-derived EB cells

value: day 4 embryoid bodies differentiation of mouse embyronic stem cells

value: hemangiogenic mesoderm-favoured


title: CRBT35 [NB_cont_25]

value: control

value: NB


title: 901361: HDM - IL4 Ab

value: lung


title: CRBT34 [NB_cont_24]


title: 901360: HDM - IL4 Ab

value: HDM


title: 901362: HDM - IL4 Ab

value: Il4hu/hu Il4rahu/hu


title: 901359: HDM - IL4 Ab


title: CRBT32 [NB_cont_21]


title: 901358: HDM - IL4Ra Ab

value: IL4Ra Ab


title: CRBT31 [NB_cont_20]


title: 901357: HDM - IL4Ra Ab


title: 901356: HDM - IL4Ra Ab


title: CRBT30 [NB_cont_18]


title: 901355: HDM - IL4Ra Ab


title: 901352: HDM - IL4Ra Ab


title: CRBT29 [NB_cont_17]


title: 901351: HDM – control hIgG

value: control hIgG


title: 901353: HDM - IL4Ra Ab


title: 901354: HDM - IL4Ra Ab


title: CRBT27 [NB_cont_15]


title: 2mo-WT-5M

value: WT

value: 2 months

value: M

value: Microglia

value: None/naïve


title: 901349: HDM – control hIgG


title: 901350: HDM – control hIgG


title: 901348: HDM – control hIgG


title: 901347: HDM – control hIgG


title: CRBT25 [NB_cont_12]

value: 8-10 weeks old

value: brain (sub-ventricular zone and corpus callosum)


title: 901346: HDM – control hIgG


title: CRBT24 [NB_cont_11]


title: CRBT23 [NB_cont_10]


title: 901345: HDM – control hIgG


title: Balb_5 day RSV_biological rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression from Balb mice exposed to 5 day RSV

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: Balb mice, 5 day post RSV infection

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours.

extract_protocol: RNA was isolated from a portion of the left lung of each mouse (n = 3/group) using the RNeasy Mini kit

treatment_protocol: Age matched inbred mice were instranasally infected with 10^6 PFU RSV L19 or HepG2 vehicle in HBSS.  Mice were sacrificed 1 and 5 days post infection.

value: Balb

value: left lung


title: Balb_1 day RSV_biological rep3

description: gene expression from Balb mice exposed to 1 day RSV

source_name: Balb mice, 1 day post RSV infection


title: Balb_5 day RSV_biological rep2


title: Balb_5 day RSV_biological rep1


title: 901344: HDM - no Ab

value: no Ab


title: CRBT22 [NB_cont_4]

value: control


title: Balb_1 day RSV_biological rep2


title: Balb_vehicle_biological rep3

description: gene expression from Balb vehicle control

source_name: Balb mice, HepG2 vehicle control


title: Balb_1 day RSV_biological rep1


title: 901342: HDM - no Ab


title: Balb_vehicle_biological rep1


title: 901340: HDM - no Ab


title: CRBT21 [Oligo_cont_27]

value: Olig2-tdTomato TH39Gsat/Mmcd

value: O


title: 901338: HDM - no Ab

value: lung

value: HDM


title: CRBT19 [Oligo_cont_12]


title: 901339: HDM - no Ab

value: Il4hu/hu Il4rahu/hu


title: 901336: Saline (no HDM)

value: Saline

value: Saline (no HDM)


title: CRBT14 [ME_cont_42]

value: lesion

value: OligNB

value: OligNBL


title: 901335: Saline (no HDM)


title: 901334: Saline (no HDM)


title: 901343: HDM - no Ab


title: 901341: HDM - no Ab


title: 901333: Saline (no HDM)


title: CRBT11 [ME_cont_37]


title: CRBT10 [ME_cont_35]


title: CRBT6 [NB_cont_26]

value: NB


title: 876652: HDM - no Ab


title: 901337: HDM - no Ab


title: 876651: HDM - no Ab


title: 876648: HDM - no Ab


title: 876650: HDM - no Ab


title: CRBT4 [NB_cont_8]

value: 8-10 weeks old


title: DBA2J_5 day RSV_biological rep3

description: gene expression from DBA2J mice exposed to 5 day RSV

source_name: DBA2J mice, 5 day post RSV infection


title: DBA2J_5 day RSV_biological rep1


title: CRBT5 [NB_cont_9]

value: brain (sub-ventricular zone and corpus callosum)


title: 876647: HDM - no Ab


title: DBA2J_5 day RSV_biological rep2


title: 876646: Saline (no HDM)


title: CRBT3 [NB_cont_7]


title: 876654: HDM – control hIgG

value: control hIgG


title: 901332: Saline (no HDM)


title: 876645: Saline (no HDM)


title: DBA2J_1 day RSV_biological rep2

description: gene expression from DBA2J mice exposed to 1 day RSV

source_name: DBA2J mice, 1 day post RSV infection

value: left lung


title: 876643: Saline (no HDM)


title: CRBT2 [NB_cont_5]


title: CRBT16 [ME_cont_49]


title: DBA2J_1 day RSV_biological rep3


title: AJ_5 day RSV_biological rep3

description: gene expression from AJ mice exposed to 5 day RSV

source_name: AJ mice, 5 day post RSV infection

value: AJ


title: AJ_5 day RSV_biological rep2


title: DBA2J_vehicle_biological rep2

description: gene expression from DBA2J vehicle control

source_name: DBA2J mice, HepG2 vehicle control


title: CRBT1 [NB_cont_2]

value: control


title: 876629: HDM – control mIgG

value: control mIgG


title: 876630: HDM – control mIgG


title: 876628: HDM – control mIgG


title: DBA2J_vehicle_biological rep1


title: Vehicle and glucose rep 3

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

description:
replicate 3
SAMPLE 180

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was log2-transformed, normalized with shift to 75 percentile and baseline transformed to median of all samples in GeneSpring 14.5 Software

label: Biotin

source_name: Mouse liver tissue

label_protocol: Biotinylated cRNA were prepared with the Illumina® Total PrepT RNA Ampification kit (Life Technologies) for Illumina arrays

extract_protocol: Total RNA from liver tissue was isolated as described previously by Trizol reagent

treatment_protocol: The mice were treated i.p. with pregnenolone-16-α-carbonitrile (PCN, 50mg/kg dissolved in DMSO-corn oil 1:3) or vehicle (DMSO-corn oil 1:3) once daily for four days. The mice were fasted for four hours and then administered glucose (2g/kg) by oral gavage or further kept on fasting. The mice were sacrificed 1 hour after glucose administration. The livers were collected and frozen in liquid nitrogen and used for total RNA extraction.

value: DMSO and glucose

value: 18 weeks

value: Liver


title: 876653: HDM - no Ab

value: lung

value: HDM

value: no Ab

value: Il4hu/hu Il4rahu/hu


title: AJ_1 day RSV_biological rep3

description: gene expression from AJ mice exposed to 1 day RSV

source_name: AJ mice, 1 day post RSV infection


title: Vehicle and glucose rep 2

description:
replicate 2
SAMPLE 179

value: 17 weeks


title: 876644: Saline (no HDM)

source_name: lung

value: Saline

value: Saline (no HDM)


title: PCN and glucose rep 3

description:
replicate 3
SAMPLE 181

value: PCN, 50mg/kg and glucose

value: 19 weeks


title: AJ_5 day RSV_biological rep1


title: Locally recurrent conjunctival melanoma [SAMPLE 59]

type: genomic

city: Liverpool

first: Sarah

middle: E

last: Coupland

address: West Derby Street

department: Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

description: Genome-wide Human SNP 6.0 array

hyb_protocol: Hybridised to Affymetrix SNP 6.0 arrays according to manufacturers protocol

scan_protocol: Arrays were scanned using the Affymetrix GeneChip 3000 7G Scanner with the GeneChip Command Console software

data_processing:
Genotypes and confidence scores were generated by fitting two-dimensional Gaussian functions to the microarray data using a customized expectation-maximization algorithm (Birdseed algorithm v. 2.0, Affymetrix). Subsequent data analysis was performed using Partek® Genomics Suite® software v. 6.6 (Partek, St. Louis, MI, USA) starting from CEL files. Considering the use of FFPE specimens and to increase the signal-to-noise ratio, probe sets from fragments longer than 700 bp were removed from further analysis (as recommended by Partek®). CN values were generated from the allele intensities using the Partek® 380-sample HapMap reference (run by Affymetrix) for unpaired samples. Starting with CN estimates for each marker, a list of regions was identified using genomic segmentation. This algorithm identified breakpoints, which represented changes in CN between adjacent regions. For the identification of different regions, a minimum of 50 genomic markers had to be included within a region and a t-test p-value threshold of 0.001 was applied. Genes overlapping the regions were identified and annotated with the NCBI Reference Sequence (RefSeq, released 03.14.16) database. After detection of CN alterations (CNAs) in all samples, Venn diagrams were used to identify genes  specifically amplified or deleted in CoM that metastasied and those without metastses. The list was further refined to include only oncogenes and TSGs as defined in UniProt (www.Uniprot.org). Further analyses of CNAs of CoM that were BRAF mutant were compared to those with NRAS  mutation. The list was further refined to include only oncogenes and TSGs as defined in UniProt.For the AsCN analysis, the AsCN workflow was used. In brief, the intensity (CEL) and genotype (CHP) files were uploaded and the AsCN was created using the unpaired analysis. AI was calculated and overlapped with the CN regions determined using the CN analysis workflow. Finally, the overlapping genes were identified and annotated with the NCBI RefSeq.
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

molecule: genomic DNA

source_name: Conjunctival melanoma

label_protocol: Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 Assay following the manufacturers protocol with the exception of doubling the number of PCR reactions to compensate for using FFPE material

extract_protocol: Qiagen DNeasy blood and tissue kit following FFPE protocol. Final purification using GenElute (Sigma) following the manaufacturer's protocol

value: Conjunctival melanoma

tag: gender

value: Male

tag: metastases

value: Present

tag: braf mutation

value: V600 E/EC

tag: nras mutation

value: Negative


title: 876626: HDM - IL4 Ab

value: IL4 Ab


title: 876627: HDM – control mIgG

value: control mIgG


title: Primary conjunctival melanoma [SAMPLE 57]

description: Genome-wide Human SNP 6.0 array

value: Female


title: PCN and glucose rep 2

description:
replicate 2
SAMPLE 178

value: 16 weeks

value: Liver


title: 876623: HDM - IL4 Ab

value: lung

value: HDM


title: Vehicle and glucose rep 1

description:
replicate 1
SAMPLE 176

value: DMSO and glucose

value: 14 weeks


title: 876622: HDM - IL4 Ab

value: Il4hu/hu Il4rahu/hu


title: Primary conjunctival melanoma [SAMPLE 56]

description: Genome-wide Human SNP 6.0 array

value: Absent


title: 876642: Saline (no HDM)

value: Saline

value: Saline (no HDM)


title: Primary conjunctival melanoma [SAMPLE 55]

description: Genome-wide Human SNP 6.0 array

value: Conjunctival melanoma

value: Male


title: AJ_vehicle_biological rep3

description: gene expression from AJ vehicle control

source_name: AJ mice, HepG2 vehicle control

value: AJ

value: left lung


title: AJ_1 day RSV_biological rep2


title: AJ_vehicle_biological rep2

description: gene expression from AJ vehicle control


title: Vehicle rep 3

description:
replicate 3
SAMPLE 170

value: DMSO

value: 13 weeks


title: DBA2J_1 day RSV_biological rep1


title: 876620: HDM - IL4 Ab

value: IL4 Ab


title: 876621: HDM - IL4 Ab


title: Primary conjunctival melanoma [SAMPLE 54]

description: Genome-wide Human SNP 6.0 array

value: Female

value: Negative


title: Vehicle rep 2

description:
replicate 2
SAMPLE 167

value: 12 weeks

value: Liver


title: 876618: HDM - IL4Ra Ab

value: lung

value: HDM

value: IL4Ra Ab


title: 876624: HDM - IL4 Ab

value: Il4hu/hu Il4rahu/hu


title: C57BL6J_5 day RSV_biological rep3

description: gene expression from C57BL6J mice exposed to 5 day RSV

source_name: C57BL6J mice, 5 day post RSV infection


title: Primary conjunctival melanoma [SAMPLE 58]

description: Genome-wide Human SNP 6.0 array

value: Absent

value: V600 E/EC


title: PCN and glucose rep 1

description:
replicate 1
SAMPLE 177

value: PCN, 50mg/kg and glucose

value: 15 weeks


title: PCN rep 2

description:
replicate 2
SAMPLE 165

value: PCN, 50mg/kg

value: 10 weeks


title: Balb_vehicle_biological rep2

value: Balb

value: left lung


title: PCN rep 1

description:
replicate 1
SAMPLE 162

value: 9 weeks


title: 876616: HDM - IL4Ra Ab


title: Locally recurrent conjunctival melanoma [SAMPLE 51]

description: Genome-wide Human SNP 6.0 array

value: Conjunctival melanoma

value: Female


title: Locally recurrent conjunctival melanoma [SAMPLE 53]

description: Genome-wide Human SNP 6.0 array

value: Present

value: Negative


title: Locally recurrent conjunctival melanoma [SAMPLE 50]

description: Genome-wide Human SNP 6.0 array

value: Male


title: PCN rep 3

description:
replicate 3
SAMPLE 166

value: 11 weeks

value: Liver


title: C57BL6J_5 day RSV_biological rep2


title: Primary conjunctival melanoma [SAMPLE 49]

description: Genome-wide Human SNP 6.0 array

value: Unknown


title: Vehicle rep 1

description:
replicate 1
SAMPLE 160

value: DMSO

value: 8 weeks


title: C57BL6J_5 day RSV_biological rep1


title: C57BL6J_1 day RSV_biological rep2

description: gene expression from C57BL6J mice exposed to 1 day RSV

source_name: C57BL6J mice, 1 day post RSV infection


title: AJ_vehicle_biological rep1

description: gene expression from AJ vehicle control

value: AJ


title: Primary conjunctival melanoma [SAMPLE 48]

description: Genome-wide Human SNP 6.0 array

value: Absent


title: 876613: HDM - IL4Ra Ab

value: lung

value: HDM

value: IL4Ra Ab

value: Il4hu/hu Il4rahu/hu


title: 876617: HDM - IL4Ra Ab


title: Primary conjunctival melanoma [SAMPLE 47]

description: Genome-wide Human SNP 6.0 array


title: Sham5

city: Farmington

first: Richard

last: Mains

state: CT

address: 263 Farmington Ave

department: Neuroscience

institute: UConn Health

description: RPKM Sham5

data_processing:
Read trimming: sickle, parameters: -l 45 -q 25
alignment: HiSat2, parameters: default
abundance estimation: htseq-count, parameters: default
RPKM
Differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values for each sample

source_name: primary dorsal root ganglion cell culture

growth_protocol: dissociated in DMEM with 10% FBS, 1% Pen-Strep, cell suspensions stored on ice until flow cytometry

extract_protocol:
FACS sorted cells (~3000 cells per sample) were extracted using Nucleospin RNA XS Kit and processed as per manufacturer's instructions
Illumina TruSeq Stranded mRNA
RNASeq samples were barcoded and all run in a single NextSeq run with 25-30 million total single end 75bp reads per sample.

treatment_protocol: Spinal cord injury or laminectomy (removal of bone and muscle only) were performed on separate groups of mice before cell culture was performed

tag: condition

value: Sham


title: C57BL6J_vehicle_biological rep3

description: gene expression from C57BL6J vehicle control

source_name: C57BL6J mice, HepG2 vehicle control

value: left lung


title: C57BL6J_1 day RSV_biological rep1


title: Primary conjunctival melanoma [SAMPLE 52]

description: Genome-wide Human SNP 6.0 array

value: Conjunctival melanoma

value: Female


title: C57BL6J_1 day RSV_biological rep3


title: 876615: HDM - IL4Ra Ab


title: Sham3

description: RPKM Sham3


title: Primary conjunctival melanoma [SAMPLE 46]

description: Genome-wide Human SNP 6.0 array


title: 876612: HDM – control hIgG

value: control hIgG


title: C57BL6J_vehicle_biological rep1


title: 876610: HDM – control hIgG


title: 876611: HDM – control hIgG


title: Locally recurrent conjunctival melanoma [SAMPLE 44]

description: Genome-wide Human SNP 6.0 array

value: Male


title: SCI5

description: RPKM SCI5

value: Spinal cord injury


title: Primary conjunctival melanoma [SAMPLE 45]

description: Genome-wide Human SNP 6.0 array


title: AKRJ_5 day RSV_biological rep3

description: gene expression from AKRJ mice exposed to 5 day RSV

source_name: AKRJ mice, 5 day post RSV infection

value: AKRJ


title: 876608: HDM – control hIgG


title: Sham1

description: RPKM Sham1


title: Sham4

description: RPKM Sham4


title: 876614: HDM - IL4Ra Ab


title: Primary conjunctival melanoma [SAMPLE 43]

description: Genome-wide Human SNP 6.0 array

value: Negative


title: 876609: HDM – control hIgG


title: AKRJ_5 day RSV_biological rep2


title: AKRJ_1 day RSV_biological rep3

description: gene expression from AKRJ mice exposed to 1 day RSV

source_name: AKRJ mice, 1 day post RSV infection


title: Sham2

description: RPKM Sham2


title: SCI2

description: RPKM SCI2


title: 876590: HDM - mIL13Ra2-Fc


title: SCI4

description: RPKM SCI4


title: Primary conjunctival melanoma [SAMPLE 40]

description: Genome-wide Human SNP 6.0 array


title: SCI1

description: RPKM SCI1


title: Primary conjunctival melanoma [SAMPLE 39]

description: Genome-wide Human SNP 6.0 array


title: AJ_1 day RSV_biological rep1


title: Primary conjunctival melanoma [SAMPLE 42]

description: Genome-wide Human SNP 6.0 array

value: Unknown


title: AKRJ_1 day RSV_biological rep1


title: N5

description: RPKM N5

value: Naive


title: Primary conjunctival melanoma [SAMPLE 38]

description: Genome-wide Human SNP 6.0 array

value: Present


title: 876592: HDM - mIL13Ra2-Fc


title: AKRJ_1 day RSV_biological rep2


title: Primary conjunctival melanoma [SAMPLE 41]

description: Genome-wide Human SNP 6.0 array

value: Absent

value: V600 E/EC


title: 876587: HDM - mIL13Ra2-Fc

value: lung

value: HDM


title: N4

description: RPKM N4


title: C57BL6J_vehicle_biological rep2


title: 876589: HDM - mIL13Ra2-Fc

value: Il4hu/hu Il4rahu/hu


title: AKRJ_5 day RSV_biological rep1


title: SCI3

description: RPKM SCI3


title: Primary conjunctival melanoma [SAMPLE 37]

description: Genome-wide Human SNP 6.0 array


title: AKRJ_vehicle_biological rep3

description: gene expression from AKRJ vehicle control

source_name: AKRJ mice, HepG2 vehicle control


title: N3

description: RPKM N3


title: Primary conjunctival melanoma [SAMPLE 36]

description: Genome-wide Human SNP 6.0 array


title: 876586: HDM - mIL13Ra2-Fc


title: N2

description: RPKM N2


title: AKRJ_vehicle_biological rep1


title: AKRJ_vehicle_biological rep2


title: 876583: HDM – control mIgG

value: control mIgG


title: Primary conjunctival melanoma [SAMPLE 35]

description: Genome-wide Human SNP 6.0 array


title: N1

description: RPKM N1


title: Primary conjunctival melanoma [SAMPLE 34]

description: Genome-wide Human SNP 6.0 array


title: Primary conjunctival melanoma [SAMPLE 33]

description: Genome-wide Human SNP 6.0 array


title: Wdr5 and p53 double KO day 2 embryoid bodies H3K4Me3 Cut & Run

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

library_source: genomic

data_processing:
Library strategy: Cut&Run
Cut&Run sequencing reads were mapped to the mm10 genome for mouse by using Bowtie2 (v2-2.2.4) with parameters “-q --phred33  --very-sensitive -p 10”.
Then, we removed duplicated reads using SAMtools (v1.5) . BAM files of mapping results were merged for the same sample using SAMtools and converted to BED format by using BEDTools.
Peaks regions were called for each sample by using MACS2 (v 2.1.0) from ATAC mapped reads with parameters "-f BAMPE -g mm -n WTEB2P53 -B -q 0.01 --extsize 147 --keep-dup auto".  Differential peaks between groups were called by MACS2 subcommand “bdgdiff”.
Homer v4.10 was employed to perform gene annotation of peaks and differential peaks.
Genome_build: mm10
Supplementary_files_format_and_content: peaks in text format

source_name: embryoid bodies

growth_protocol: Rx:GFP mESCs were induced to differentiation with SFEBq method (5%KSR in GMEM media)

extract_protocol:
Cut & Run experiments were performed using 2 µg anti-WDR5, anti-P53 or anti-H3K4Me3 antibody for 2X10^6 cells according to Cut & Run protocols.
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

treatment_protocol: Doxcycline was removed during differenation (EB day 0). 2% matrigel added at EB day 1.

tag: cell type

value: embryoid bodies

value: Wdr5 and p53 double KO

tag: cell line background

value: Embryonic stem cell Rx:GFP KI


title: Primary conjunctival melanoma [SAMPLE 32]

description: Genome-wide Human SNP 6.0 array

value: Conjunctival melanoma

value: Female


title: Wdr5 KO day 2 embryoid bodies H3K4Me3 Cut & Run

value: Wdr5 KO


title: Primary conjunctival melanoma [SAMPLE 31]

description: Genome-wide Human SNP 6.0 array

value: Male


title: Wdr5 and p53 double KO day 2 embryoid bodies WDR5 Cut & Run rep2


title: Primary conjunctival melanoma [SAMPLE 30]

description: Genome-wide Human SNP 6.0 array

value: Negative


title: Primary conjunctival melanoma [SAMPLE 29]

description: Genome-wide Human SNP 6.0 array


title: OCM1.OE.NC.RNA-seq

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: OCM1.OE.HINT2.and.OCM1.OE.NC.RNA-seq.processed.data.xlsx

data_processing:
For RNA-seq and MeRIP-seq, reads were processed using Cutadapt software (version 1.18) and Trimmomatic (version 0.36). The remained reads were aligned to human genome (version hg19) using Hisat2 (version 2.1.0).
For MeRIP-seq data, MACS2 software (version 2.0.10) was used for m6A peak calling, and m6A peaks were annotated by perfroming BEDTools’ intersectBed (version 2.27.1).
For miCLIP-seq, pre-processing was performed by using CLIP Tool Kit (CTK). The remined reads were aligned to human genome (version hg19) using BWA software (version 0.7.10).
m6A locus were detected by performing Program CIMS.pl for miCLIP-seq data.
miCLIP-seq m6A locus were annotated by using BEDTools’ intersectBed (version 2.27.1).
Genome_build: hg19
Supplementary_files_format_and_content: miCLIP-seq_m6A_single-nucleotide-resolution_locus.xlsx.gz: miCLIP-seq_m6A_single-nucleotide-resolution_locus
Supplementary_files_format_and_content: MeRIP-seq_m6A_peak_locus.xlsx.gz: MeRIP-seq_m6A_peak_locus
Supplementary_files_format_and_content: Reads_count_featureCounts.xlsx.gz: Reads count for all samples

source_name: Ocular melanoma cell line

extract_protocol:
For RNA-seq, total RNA was extracted from samples using an EZ-press RNA Purification Kit (B0004).
For miCLIP-seq, mRNA was isolated from tumor and normal cell lines by using Dynabeads mRNA Purification Kit (Life Technologies, 61006).
For RNA-seq, libraries were constructed from  100 ng of total RNA using an Illumina TruSeq RNA Sample Prep Kit (San Diego, CA, USA) following the manufacturer’s protocol.
For MeRIP-seq, purified mRNA was randomly fragmented to approximately 100 nucleotides using Ambion RNA fragmentation reagents and then subjected to IP with an anti-m6A antibody (202003, Synaptic Systems) and protein A magnetic beads (88845, Pierce) in meRIP buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.4, 0.1% NP-40) supplemented with RNase inhibitor. m6A-containing mRNA fragments were eluted with m6A in MeRIP buffer and purified using TRIzol reagent.
For miCLIP-seq, mRNA was fragmented to ~100 nucleotides using fragmentation reagent (Life Technologies, AM8740), and incubated with 5 µg of an anti-m6A antibody (Abcam, ab151230) in 450 µL of IP buffer (50 mM Tris, 100 mM NaCl, 0.05% NP-40, adjusted to pH 7.4) under gentle rotation at 4°C for 2 h. The mixture was transferred to a clear flat-bottom 96-well plate (Corning) on ice and irradiated three times with 0.15 J/cm2 at 254 nm using a CL-1000 Ultraviolet Crosslinker (UVP). After irradiation, the mixture was collected and incubated with 50 µL of prewashed Dynabeads Protein A (Life Technologies, 1001D) at 4°C for 2 h. After extensive washing twice with high-salt buffer (50 mM Tris, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, adjusted to pH 7.4) and twice with IP buffer, the samples on the beads were subjected to dephosphorylation with T4 PNK (NEB, M0201L) at 37°C for 20 min. The RNA was then eluted from the beads by proteinase K (Sigma, P2308) treatment at 55°C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. The purified RNA was subjected to library construction using SMARTer smRNA-Seq Kit for Illumina (Clontech Laboratories, 635030) according to the manufacturer’s instructions.

value: Ocular melanoma cell


title: TA Stressed

city: Deagu

first: Young-Saeng

last: Kim

address: 80, Daehak-ro

country: South Korea

institute: Kyungpook National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to S.elongatus PCC7942 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/430?genome_assembly_id=300122
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: Cyanobacterial cell

growth_protocol: Initial absorbances at 730 nm (A730) were adjusted to 0.03. Aliquots of each sample were then measured to adjust them to 0.03 in BG11 medium after culturing for 18 days at 30°C with shaking in liquid microbial lab flasks

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). rRNA was removed using Ribo-Zero Magnetic kit (epicentre, Inc., USA) from each 5ug of total RNA.
RNA libraries were prepared for sequencing using Clontech SMARTer Stranded RNA-Seq Kit standard protocols.

treatment_protocol: Responses to oxidative stress were evaluated by allowing cells to reach the exponential phase (A730 = 0.3–0.35) before exposing them to 2.5 mM H2O2 at 7 days with shaking, after which A730 values were monitored each day through the end of the experiment.

tag: strain

tag: genotype/variation

value: transgenic microalgae (TA)

value: stressed; 2.5 mM H2O2 at 7 days


title: TA Normal

value: normal


title: WT Normal

value: wild type


title: Primary conjunctival melanoma [SAMPLE 28]

description: Genome-wide Human SNP 6.0 array

tag: tissue

value: Absent


title: Wdr5 and p53 double KO day 2 embryoid bodies P53 Cut & Run rep2


title: Wdr5 and p53 double KO day 2 embryoid bodies WDR5 Cut & Run rep1


title: Wdr5 and p53 double KO day 2 embryoid bodies P53 Cut & Run rep1


title: Primary conjunctival melanoma [SAMPLE 27]

description: Genome-wide Human SNP 6.0 array

value: Unknown


title: OCM1.sgNC.RNA-seq

description: OCM1.sgALKBH5.and.OCM1.sgNC.RNA-seq.processed.data.xlsx


title: OCM1.OE.HINT2.RNA-seq


title: WT day 2 embryoid bodies H3K4Me3 Cut & Run

value: WT


title: WT day 2 embryoid bodies P53 Cut & Run  rep2


title: Primary conjunctival melanoma [SAMPLE 26]

description: Genome-wide Human SNP 6.0 array

value: Present

value: V600 E/EC


title: 876584: HDM – control mIgG

value: lung

value: HDM

value: control mIgG

value: Il4hu/hu Il4rahu/hu


title: WT day 2 embryoid bodies WDR5 Cut & Run rep2

value: embryoid bodies

value: Embryonic stem cell Rx:GFP KI


title: 876588: HDM - mIL13Ra2-Fc


title: Primary conjunctival melanoma [SAMPLE 25]

description: Genome-wide Human SNP 6.0 array

value: Conjunctival melanoma

value: Female

value: Negative


title: PIG1.shNC.RNA-seq

description: PIG1.shMETTL3.and.PIG1.shNC.RNA-seq.processed.data.xls

source_name: Melanocyte cell line

value: Melanocyte cell


title: 1030444: IL-13 + (Fel d 1 IgE + Fel d 1)

source_name: bone marrow-derived mast cells

value: bone marrow-derived mast cells

value: IL-13 + (Fel d 1 IgE + Fel d 1)


title: WT Stressed

value: wild type

value: stressed; 2.5 mM H2O2 at 7 days


title: 1030445: IL-13 + (Fel d 1 IgE + Fel d 1)


title: WT day 2 embryoid bodies P53 Cut & Run rep1

value: WT


title: PIG1.shMETTL3.RNA-seq


title: Primary conjunctival melanoma [SAMPLE 24]

description: Genome-wide Human SNP 6.0 array

value: Absent


title: WT day 2 embryoid bodies WDR5 Cut & Run rep1


title: 1030443: IL-13 + (Fel d 1 IgE + Fel d 1)


title: PIG1.MeRIP-seq.IP


title: 1030442: IL-13 + (Fel d 1 IgE + Fel d 1)


title: Primary conjunctival melanoma [SAMPLE 23]

description: Genome-wide Human SNP 6.0 array

value: Male

value: Present

value: V600 E/EC


title: PIG1.MeRIP-seq.Input


title: Primary conjunctival melanoma [SAMPLE 22]

description: Genome-wide Human SNP 6.0 array


title: Locally recurrent conjunctival melanoma [SAMPLE 21]

description: Genome-wide Human SNP 6.0 array


title: OCM1.sgALKBH5.RNA-seq

value: Ocular melanoma cell


title: 1030441: IL13


title: OCM431.MeRIP-seq.IP


title: Retina 6m APP/PS1 Rep5

first: Asli

last: Uyar

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

data_processing:
Sequenced reads were quality trimmed and filtered using Trimmomatic tool and reads passing the quality filtering were mapped to the mouse mm10 reference genome using ‘bowtie’ algorithm.
HTSeq Python package was used to calculate raw read counts per transcript.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts values for each Sample ...

source_name: Retina

extract_protocol:
Left retinas and left brain hemispheres were dissected and snap frozen for preservation of RNA for gene expression studies. Total RNA was extracted using Trizol (Invitrogen, CA).
mRNA was purified from total RNA using biotin-tagged poly dT oligonucleotides and streptavidin-coated magnetic beads and quality was assessed using an Agilent Technologies 2100 Bioanalyzer.

tag: age

value: 6 months

value: female


title: Retina 6m APP/PS1 Rep2


title: 1030439: IL13


title: Retina 6m APP/PS1 Rep3


title: OCM1a.MeRIP-seq.IP


title: OCM431.MeRIP-seq.Input


title: 1030438: IL13


title: 1030440: IL13


title: Primary conjunctival melanoma [SAMPLE 18]

description: Genome-wide Human SNP 6.0 array

value: Unknown


title: 1030437: IL4 + (Fel d 1 IgE + Fel d 1)

value: IL4 + (Fel d 1 IgE + Fel d 1)


title: OCM1a.MeRIP-seq.Input


title: Primary conjunctival melanoma [SAMPLE 17]

description: Genome-wide Human SNP 6.0 array

value: Conjunctival melanoma


title: Retina 2m APP/PS1 Rep5

value: 2 months


title: Retina 2m APP/PS1 Rep4


title: Primary conjunctival melanoma [SAMPLE 16]

description: Genome-wide Human SNP 6.0 array

value: Negative


title: OCM1.MeRIP-seq.Input


title: 1030435: IL4 + (Fel d 1 IgE + Fel d 1)

value: bone marrow-derived mast cells


title: Retina 2m APP/PS1 Rep3


title: Primary conjunctival melanoma [SAMPLE 20]

description: Genome-wide Human SNP 6.0 array

value: Female


title: CRMM1.MeRIP-seq.IP


title: 1030434: IL4 + (Fel d 1 IgE + Fel d 1)


title: Primary conjunctival melanoma [SAMPLE 15]

description: Genome-wide Human SNP 6.0 array


title: Primary conjunctival melanoma [SAMPLE 14]

description: Genome-wide Human SNP 6.0 array


title: Retina 2m APP/PS1 Rep2


title: Primary conjunctival melanoma [SAMPLE 19]

description: Genome-wide Human SNP 6.0 array


title: Retina 2m APP/PS1 Rep1


title: 1030433: IL4


title: CM2005.1.MeRIP-seq.IP


title: Retina 6m WT Rep6


title: CRMM1.MeRIP-seq.Input


title: Retina 6m APP/PS1 Rep1


title: OCM1.MeRIP-seq.IP


title: 1030432: IL4


title: CM2005.1.MeRIP-seq.Input


title: Primary conjunctival melanoma [SAMPLE 12]

description: Genome-wide Human SNP 6.0 array


title: Primary conjunctival melanoma [SAMPLE 13]

description: Genome-wide Human SNP 6.0 array


title: 1030436: IL4 + (Fel d 1 IgE + Fel d 1)


title: 1030431: IL4


title: Retina 6m APP/PS1 Rep4


title: Retina 6m WT Rep5


title: 3T3L1-24hEtOH-3

city: Stanford

first: Peter

middle: K

last: Jackson

state: CA

address: 279 Campus Dr., CCSR 3230

institute: Stanford University

data_processing:
Sequencing data QC was performed using fastqc and trimmomatic. Aligment was done using star aligner (STAR_2.5.1b) to GRCm38.p5. Transcripts counts were determined using either cuffdiff (cuffdiff v2.2.1) or htseq (htseq-count version 0.9.1) using gencode M14 annotattions (gencode.vM14.annotation.gtf). In addition, fastq files were also analyzed using kallisto (kallisto 0.43.1) using mm38.p5_ncbi_rna_transscripts.idx.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text, expression values (counts/fpkm)

source_name: 3T3L1 cells

growth_protocol: 3T3-L1 cells were grown to confluency in DMEM containing 10% Bovine Calf Serum, followed by another 2 days at confluency in DMEM containing 10% Bovine Calf Serum.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit
random-primed pcr
paired-end sequencing, Sequencing data was generated on an Illumina HiSeq4000

treatment_protocol: 3T3-L1 cells were grown to confluency, kept confluency-arrested for 2 days, and differentiated in triplicates using historical differentiation cocktail, ctrl (-DHA) differentiation cocktail, or DHA cocktail.

value: 3T3L1 cells


title: Primary conjunctival melanoma [SAMPLE 11]

description: Genome-wide Human SNP 6.0 array


title: 1030430: IL4


title: 3T3L1-24hEtOH-2


title: Retina 6m WT Rep4


title: Primary conjunctival melanoma [SAMPLE 10]

description: Genome-wide Human SNP 6.0 array


title: Primary conjunctival melanoma [SAMPLE 9]

description: Genome-wide Human SNP 6.0 array


title: 3T3L1-24hEtOH-1


title: 1030428: (Fel d 1 IgE + Fel d 1)

value: (Fel d 1 IgE + Fel d 1)


title: Retina 6m WT Rep3

value: WT


title: 3T3L1-24hDM-3


title: Retina 6m WT Rep2


title: 1030429: (Fel d 1 IgE + Fel d 1)


title: Primary conjunctival melanoma [SAMPLE 7]

description: Genome-wide Human SNP 6.0 array

value: Absent


title: 3T3L1-24hDM-2


title: 3T3L1-24hDHA-3


title: Primary conjunctival melanoma [SAMPLE 8]

description: Genome-wide Human SNP 6.0 array

value: Male


title: Retina 6m WT Rep1


title: 1030426: (Fel d 1 IgE + Fel d 1)


title: 1030427: (Fel d 1 IgE + Fel d 1)


title: Primary conjunctival melanoma [SAMPLE 6]

description: Genome-wide Human SNP 6.0 array


title: Retina 2m WT Rep3


title: 3T3L1-24hDHA-2


title: Primary conjunctival melanoma [SAMPLE 4]

description: Genome-wide Human SNP 6.0 array


title: 1030423: no treatment

value: no treatment


title: Locally recurrent conjunctival melanoma [SAMPLE 5]

description: Genome-wide Human SNP 6.0 array


title: 3T3L1-24hDM-1


title: Retina 2m WT Rep2


title: 1030424: no treatment


title: 1030425: no treatment


title: Retina 2m WT Rep5


title: Primary conjunctival melanoma [SAMPLE 3]

description: Genome-wide Human SNP 6.0 array


title: Retina 2m WT Rep4


title: 1030422: no treatment


title: 3T3L1-24hDHA-1


title: Retina 2m WT Rep1


title: 3T3L1-0h-2


title: Brain 6m APP/PS1 Rep5

source_name: Whole brain


title: Primary conjunctival melanoma [SAMPLE 2]

description: Genome-wide Human SNP 6.0 array

source_name: Conjunctival melanoma


title: 3T3L1-0h-1


title: Primary conjunctival melanoma [SAMPLE 1]

description: Genome-wide Human SNP 6.0 array


title: AML5 clone expressing sgEPCR-UM171-2

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: ARN (mRNA-Seq stranded/ Transcriptome)

data_processing:
Sequencing was performed with the Illumina HiSeq 2000 and basecalls analyzed using Illumina RTA 1.17.21.3.
Samples demultiplexed using Illumina Casava 1.8.2 using adapter masking.
Sequenced reads were trimmed for masked adapters and low quality extremities using Trimmomatic 0.35 and then mapped to the reference genome using STAR version 2.5.1b, guided by transcript annotations from Gencode version 26.
Expression values were computed using RSEM version 1.2.28 and Gencode version 26 annotations (based on Ensembl 88).
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output (first line identifies the columns)

source_name: AML5 clone expressing sgEPCR (EPCR null) exposed to UM171 (500nM)  for 24h_2

growth_protocol: AMl5 cell line cultured in DMEM/10% FBS and exposed to UM171 or DMSO for 6h, 24h, 48h or 72h.

extract_protocol:
Trizol extraction and Qiagen Rneasy column purification
KAPA RNA Stranded PolyA

treatment_protocol: UM171 were used at 500nM

tag: cell line

value: EPCR knockdown

tag: time


title: AML5 clone expressing sgEPCR-UM171-3

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 clone expressing sgEPCR (EPCR null) exposed to UM171 (500nM)  for 24h_3

tag: treatment


title: Brain 6m APP/PS1 Rep4

tag: Sex


title: AML5 clone expressing sgEPCR-DMSO-3

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 clone expressing sgEPCR (EPCR null) exposed to DMSO for 24h_3

tag: genotype

value: DMSO


title: Brain 6m APP/PS1 Rep2

value: 6 months


title: Brain 6m APP/PS1 Rep1

value: female


title: Brain 6m APP/PS1 Rep3


title: AML5 clone expressing sgEPCR-UM171-1

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 clone expressing sgEPCR (EPCR null) exposed to UM171 (500nM)  for 24h_1


title: Brain 5m APP/PS1 Rep11

value: 5 months


title: RNA-seq_LacZ_10hpf_1

city: New York

first: Lionel

last: Christiaen

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: New York University

data_processing:
ATAC-seq reads were trimmed using trim_galore version 0.4.4 with parameters --nextera --paired –three_prime_clip_R1 1 --three_prime_clip_R2 1
ATAC-seq reads were aligned using Bowtie2 version 2.3.2 with parameters –no-discordant --no-mixed -N 1 -X 1000
RNA-seq reads were aligned using STAR version 2.5.3a with parameters --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts TranscriptomeSAM --bamRemoveDuplicatesType UniqueIdentical
Reads were filtered to remove duplicates, mitochondrial reads, and quality score less than 30
ATAC-seq peaks were called using macs2 version 2.1.1 with gDNA as the input control and parameters  --nomodel -g 1.15e8 --keep-dup all --shift -29 --extsize 50 --bdg --call-summits
Genome_build: kh2013
Supplementary_files_format_and_content: bigWig files were generated using deepTools version 2.4.2 with parameters --centerReads --normalizeUsingRPKM --bs 10; Scores represent read density normalized by RPKM
Supplementary_files_format_and_content: Read counts for merged ATAC-seq peaks were generated using bedtools version 2.26.0
Supplementary_files_format_and_content: Read counts for RNA-seq were generated using HTSeq version 0.6.1p1 with parameters -r pos -i gene_id

organism: Ciona robusta

source_name: ATM+TVC

growth_protocol: Gametes from several Ciona adults were collected separately for in vitro cross-fertilization followed by dechorionation and electroporation. Electroporated eggs were cultured in filtered artificial seawaterin  agarose-coated plastic Petri dishes at 18°C.

extract_protocol:
Nulcei were isolated from FACSorted cells and incubated in the tagmentation reaction. Tagmented-chromatin fragmented were PCR amplified and purified. The quality of ATAC-seq libraries was assessed by using 2100 Bioanalyzer (Agilent Technologies).
ATAC-seq was performed with minor modifications to the published protocol (Buenrostro et al., 2013). 3000-5000 cells obtained by FACS were centrifuged at 800 x g for 4 min at 4 °C for each sample. Cells were resuspended in 5 µL of cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 nM NaCL, 3 nM MgCl2, 0,1% v/v Igepal CA-360 [Sigma-Aldrich] and incubated on ice for 5 min. After centrifugation of the cells at 500 x g for 10 min at 4 °C, the supernatant was discarded.  The tagmentation reaction was performed at 37 °C for 30 min using Nextera Sample Preparation kit (Illumina). After tagmentation, transposed DNA fragments were amplified using the following PCR condition: 1 cycle of 72°C for 5 min and 98°C for 30 s, followed by 12 to 14 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Amplified libraries were purified using PCR purification MinElute kit (Qiagen), and the quality of of the purified library was assessed by using 2100 Bioanalyzer (Agilent Technologies) and a High Sensitivity DNA analysis Kit (Agilent Technologies) to confirm a period pattern in the size of the amplified DNA. After size selection by using Agencourt Ampure XP beads (Beckman Coulter, Cat#A633880) with a bead-to-sample ratio of 1.8:1, the libraries were sequenced as paired-end 50 bp by using the HiSeq 2500 platform (Illumina) according to the manufacturer’s instructions. An input control was also generated by using 10 ng of C. robusta genomic DNA.

treatment_protocol: Different quantities of plasmids were electroporated depending on the constructs: the amount of fluorescent reporter DNA (Mesp>nls::lacZ, Mesp>hCD4::mCherry, Mesp>tagRFP, MyoD905>EGFP and Hand-r>tagBFP) and NLS::lacZ was typically 50 μg, but only 15 µg for Mesp-1>H2B::mCherry. For perturbation constructs (Mesp>Fgfr, Mesp>Mek, Foxf>M-RasCA, Hand-r>FgfrDN),  70 µg were usually electroporated, except for Mesp>nls::Cas9-Gem::nls (30 µg) and pairs of U6 >sgRNA plasmids (25 µg each).

value: control

tag: cell lineage

tag: omit

value: FALSE

tag: method

tag: ko

tag: date


title: RNA-seq_Ngn_KO_10hpf_1

tag: condition

value: TRUE


title: RNA-seq_Ngn_KO_10hpf_2


title: RNA-seq_LacZ_10hpf_2


title: AML5 clone expressing sgEPCR-DMSO-1

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 clone expressing sgEPCR (EPCR null) exposed to DMSO for 24h_1


title: AML5 clone expressing sgEPCR-DMSO-2

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 clone expressing sgEPCR (EPCR null) exposed to DMSO for 24h_2


title: AML5-U72-2

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 72h_2


title: RNA-seq_FoxF_KO_10hpf_1


title: RNA-seq_FoxF_KO_10hpf_2


title: Brain 5m APP/PS1 Rep9


title: AML5-U72-3

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 72h_3


title: Brain 5m APP/PS1 Rep8


title: MekMut_18hpf_3

source_name: ASM+SHP+FHP

value: new


title: Brain 5m APP/PS1 Rep10


title: AML5-U6-3

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 6h_3


title: AML5-U6-2

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 6h_2


title: Naïve_rep2

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: Hybridisations were performed by Ark Genomics using Gene Titan hardware.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: CEL files were processed using Bioconductor packages (e.g. oligo, pd.mogene.2.1.st, affy, mogene21sttranscriptcluster.db) to acquire, QC assess, and normalise sample data prior to the relevant group-wise comparisons being performed using limma.

source_name: Naïve Spleen

label_protocol: Cy3 labelled cDNA was prepared using the NuGen Ovation Pico SL kit

growth_protocol: The parathymic, posterior, mediastinal and paravertebral LN, were taken as a source of tLN draining the PleC.

extract_protocol: RNAeasy kit (Qiagen) as per manufacturers instructions

treatment_protocol: PleC cells were recovered by lavage. tLN cells were dissociated and washed in RPMI-1640 (invitrogen) supplemented with 0.5% mouse sera (Caltag-Medsystems), 100 U/ml penicillin, 100 μg/ ml streptomycin and 2 mM L-glutamine.

value: Naïve Spleen

tag: cell sort


title: Brain 5m APP/PS1 Rep6


title: Naïve_rep4


title: Naïve_rep3


title: MekMut_18hpf_2


title: Naïve_rep1


title: MekMut_18hpf_1


title: Brain 5m APP/PS1 Rep5


title: Nb_tLN_d6_rep5

description: Nippo

source_name: Thoracic lymph node, d6 N. brasiliensis infection

value: Thoracic lymph node

tag: time point

tag: agent

value: N. brasiliensis


title: Naïve_rep5


title: Nb_tLN_d6_rep4

description: Nippo


title: Nb_tLN_d6_rep3

description: Nippo


title: AML5-U72-1

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 72h_1


title: AML5-U48-3

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 48h_3


title: Brain 5m APP/PS1 Rep4

source_name: Whole brain


title: AML5-U48-2

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 48h_2


title: Nb_tLN_d6_rep2

description: Nippo


title: LacZ_20hpf_1

value: old


title: Brain 5m APP/PS1 Rep7


title: Ls_d60_tLN_rep4

description: Lito

source_name: Thoracic lymph node, d60 L. sigmodontis infection

value: L. sigmodontis


title: Nb_tLN_d6_rep1

description: Nippo


title: LacZ_18hpf_4


title: AML5-U6-1

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 6h_1


title: LacZ_20hpf_2


title: Brain 5m APP/PS1 Rep3


title: Ls_d60_tLN_rep3

description: Lito


title: AML5-U24-3

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 24h_3


title: Brain 5m APP/PS1 Rep2


title: AML5-U48-1

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 48h_1


title: Brain 4m APP/PS1 Rep5

value: 4 months


title: Brain 5m APP/PS1 Rep1


title: LacZ_18hpf_3


title: Ls_d60_tLN_rep5

description: Lito


title: Brain 4m APP/PS1 Rep4


title: LacZ_18hpf_2


title: LacZ_18hpf_1


title: AML5-U24-2

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 24h_2


title: AML5-U24-1

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to UM171 (500nM) for 24h_1


title: LacZ_15hpf_2

source_name: sTVC+FHP


title: AML5-DMSO-3

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to DMSO for 72h_3


title: Ls_d60_tLN_rep2

description: Lito


title: Ls_d60_PleC_rep4

description: Lito

source_name: Pleural cavity, d60 L. sigmodontis infection

value: Pleural cavity


title: AML5-DMSO-2

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to DMSO for 72h_2


title: Brain 4m APP/PS1 Rep2


title: AML5-DMSO-1

description: ARN (mRNA-Seq stranded/ Transcriptome)

source_name: AML5 exposed to DMSO for 72h_1


title: LacZ_15hpf_1


title: gfp_20hpf_1

source_name: ASM+SHP+FHP

value: mesenchyme


title: gfp_18hpf_4


title: EBL.D.d12

city: Amsterdam

first: Emile

last: van den Akker

address: Plesmanlaan 126

country: Netherlands

institute: Sanquin Blood Supply

description: Differentiation_CPM.txt,  Differentiation_TPM.txt

data_processing:
Illumina base caller v1.9
Reads were aligned using STAR with following settings
Countdata from STAR was processed using EdgeR package. Lowly expressed genes filter ( 3< cpm in at least 18 out of 40 samples)
For comparrison with ex-vivo cells SALMON was used to align and generate library and transcirpt size corrected counts (TPM)
Genome_build: ChGR38.v85
Supplementary_files_format_and_content: Tab-delimited txt files include raw count data from STAR and transcript per million from SALMON

source_name: Peripheral blood monocytes

growth_protocol: Erythroid cells expanded in Cellquin culture medium supplemented with SCF, EPO and dexamethasone.

extract_protocol:
Trizol RNA extraction
Library prep on amplified cRNA using HyperPrep Kit with RiboErase (KAPA Biosystems, Pleasanton, CA, USA) according to manufactures protocol

treatment_protocol: After exchanging expansion medium for differentiation medium daily samples were taken for RNA isolation and sequencing

tag: donor id

value: D

tag: cell type

value: Erythroid

value: 12 days of differentiation


title: Brain 4m APP/PS1 Rep1

tag: age

value: female


title: Brain 2m APP/PS1 Rep4

value: 2 months


title: Brain 2m APP/PS1 Rep5


title: Ls_d20_tLN_rep5

description: Lito

source_name: Thoracic lymph node, d20 L. sigmodontis infection

tag: tissue


title: Ls_d60_tLN_rep1

description: Lito


title: Ls_d20_tLN_rep2

description: Lito


title: gfp_18hpf_3

value: control

tag: time


title: Brain 4m APP/PS1 Rep3


title: EBL.D.d9

value: 9 days of differentiation


title: EBL.D.d7

value: 7 days of differentiation


title: Ls_d20_tLN_rep3

description: Lito


title: Brain 6m WT Rep7

value: 6 months

value: WT


title: Brain 2m APP/PS1 Rep2


title: Ls_d20_tLN_rep1

description: Lito

value: Thoracic lymph node


title: Brain 6m WT Rep6


title: gfp_18hpf_1

value: FALSE


title: Ls_d60_PleC_rep2

description: Lito


title: gfp_15hpf_1

value: old


title: Brain 2m APP/PS1 Rep1


title: Brain 6m WT Rep5


title: Ls_d20_tLN_rep4

description: Lito

value: L. sigmodontis


title: EBL.D.d6

value: 6 days of differentiation


title: Ls_d20_PleC_rep1

description: Lito

source_name: Pleural cavity, d20 L. sigmodontis infection

value: Pleural cavity


title: Brain 6m WT Rep4

source_name: Whole brain


title: Project10_bulk

city: Minneapolis

first: Zohar

last: Sachs

state: MN

address: 420 Delaware Street SE MMC 480

department: Department of Medicine, Division of Hematology, Oncology and Transplantation

institute: University of Minnesota Twin Cities

description: bulk RNA-seq

data_processing:
FastQC is run on each fastq file to generate sequence quality plots. Sequence adaptors and low-quality sequence were removed using Trimmomatic (v0.32). Trimmed reads were mapped with TOPHAT 2.0 (v2.0.10) to the mouse reference genome (UCSC GRCm38/mm10 assembly). An additional chromosome was added to the reference genome that contained the transgenes that were expressed in the mouse model (NRASG12V, MLL-AF9 and EGFP)1. Insertion size metrics were calculated for each sample using Picard software (version 1.126). Samtools software (version 1.0_BCFTools_HTSLib)2 was used to sort and index the bam files.  Cuffquant (Cufflinks version 2.2.1)3 was used to generate transcript abundance files (options used include the multi-read-correct). Murine cells with less than 75% alignment to the genome were omitted from further analysis. Each cell expressed a minimum of 1,300 genes. There were 42, 33, and 51 evaluable cells in the discovery data set, validation dataset, and Ras-off dataset, respectively. Human cells were analyzed to omit outliers per SINGuLAR Analysis Toolkit (Fluidigm). This approach identifies cells whose expression of the most commonly expressed genes exceeds the 15th percentile; cells that meet this criterion are included in the analysis, the remaining cells are omitted as outliers. In the human dataset, 25 cells were included in the analysis. After mapping and abundance estimates were completed, Cuffnorm (Cufflinks version 2.2.1)3 was used to generate fragments per kilobase of transcript per million mapped reads (FPKM) values.
Genome_build: mm10 and GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each single cell sample or bulk RNA

source_name: Bone Marrow

extract_protocol:
Primary murine NRASG12V/Mll-AF9 AMLs were harvested from spleens of leukemic mice, stained with antibodies for cell surface markers, and sorted on a FACAria (Becton Dickinson, Franklin Lakes, NJ). Cryopreserved bone marrow aspirates from healthy volunteers were purchased from Lonza (Basel, Switzerland). AML samples with >50% bone marrow blasts were obtained from the University of Minnesota Hematological Malignancies Tissue Bank in accordance with the University of Minnesota Institutional Review Board (IRB #1506E72802 and #0611M96846).Fresh AML bone marrow aspirates were CD34-selected using EasySep Magnet and EasySep Human CD34 antibody kit (StemCell Technologies, Vancouver, BC, Canada). Human AML and normal bone marrow were sorted to isolate CD34+CD38- cells. Sorted or magnet-selected cells were stained with a Live/Dead Viability and Cytotoxicity dye (Life Technologies, Carlsbad, California, # L-3224) and loaded at 250 cells/l for single-cell capture on the C1 Single-Cell Auto Prep Integrated Fluidic Circuit for small cells (5-10 m, Fluidigm, South San Francisco, California).
Captured cells were imaged to identify single, live cells for cDNA preparation. SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Takara Bio, Kusatsu, Shiga Prefecture, Japan) was used to prepare cDNA for sequencing. Fluidigm Reverse Transcription Master mix was used to prepare cDNA for PCR.

value: Leukemia stem cells

value: Bone Marrow

tag: disease state

value: acute myeloid leukemia (AML)


title: Brain 2m APP/PS1 Rep3

tag: Sex


title: gfp_10hpf_3

source_name: ATM+TVC

value: mesenchyme

value: new


title: Ls_d20_PleC_rep4

description: Lito


title: Ls_d60_PleC_rep1

description: Lito


title: EBL.D.d5

value: D

value: Erythroid

value: 5 days of differentiation


title: gfp_10hpf_2

value: control


title: Ef1a_10hpf_1

source_name: embryo


title: EBL.D.d1

value: 1 days of differentiation


title: gDNA

source_name: input control

value: TRUE


title: Brain 6m WT Rep2

value: 6 months

tag: genotype

value: WT

value: female


title: gfp_15hpf_2

tag: cell lineage

value: FALSE

value: old


title: Ls_d20_PleC_rep2

description: Lito

value: Pleural cavity

value: L. sigmodontis


title: GSC23 5' CTCF boundary 4C-seq

city: Cleveland

last: Scacheri

state: OH

address: 2109 Adelbert Road

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Library strategy: 4C-seq
4Cseqpipe was used from from van de Werken et al. Nature Methods 2012 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain the near cis counts. From the 4cseqpipe manual "Median ... of normalized contact intensity in 1kb windows. Column 1: the starting coordinate of the 1kb bin.; Column 2: the median of values within a 2kb window, centered on the 1kb genomic bin.; column 3 the 80th quantile of values in the window; column 4: the 20th quantile of values in the window; Column 5-148 as columns 2-4, but with increasing window size, going up to 50kb."

growth_protocol: Glioblastoma stem cell cultures were grown as neurospheres as previously described (Bao et al. Nature 2006). Briefly, the incubator is set at 37C, 20% oxygen, and 5% CO2. They are grown in neurobasal media minus phenol red (Thermo) supplemented with 1x B27, 100 U/mL pen/strep, 2 mM glutamine, 20ng/mL FGF, 20 ng/mL EGF, and 1mM sodium pyruvate.

extract_protocol:
DNA was extracted with standard laboratory tecniques.
Libraries were prepared according previous methods (Splinter et al. Methods 2012). Briefly, cells were crosslinked with formaldehyde and lysed to extract nuclei then digested with DpnII and ligated with T4 DNA ligase. Next, crosslinks were reversed with proteinase K at 65C. After, the DNA was digested with CviQI and ligation. Libraries were prepared from the circular DNA with PCR amplification with custom oligos detailed in Splinter et al. and designed for the particular 4C anchoring point. Libraries were cleaned with PCR Clean Dx beads before sequencing on a Illumina HiSeq 2500.

value: glioblastoma patient-derived cell model

tag: cell model id

tag: egfr amplification status

value: unamplified

tag: cutting enzymes

value: DpnII, CviQI


title: EBL.D.d0

value: 0 days of differentiation


title: gfp_10hpf_1

value: mesenchyme

tag: omit

tag: method

value: new

tag: ko

tag: date


title: EBL.D.d3

value: D

value: Erythroid

value: 3 days of differentiation


title: Project10_single cells

description: 76(forward and reverse) fastq files for 37 single cell data and 1 bulk data

value: Leukemia stem cells

value: Bone Marrow

value: acute myeloid leukemia (AML)


title: GSC23 EGFR enhancer 1 4C-seq


title: Brain 6m WT Rep1

value: 6 months

value: WT

value: female


title: Ef1a_10hpf_2

tag: condition

value: control

value: FALSE


title: Ls_d20_PleC_rep5

description: Lito

value: Pleural cavity

tag: time point

tag: agent

value: L. sigmodontis

tag: cell sort


title: EBL.D.d2

tag: donor id

tag: cell type

value: 2 days of differentiation


title: Brain 6m WT Rep3

tag: age


title: Brain 5m WT Rep12

value: 5 months

tag: Sex


title: EBL.C.d9

value: C

tag: time

value: 9 days of differentiation


title: dnFGFR_20hpf_1

tag: cell lineage

value: TRUE

value: old


title: EBL.D.d4

value: D

value: Erythroid

value: 4 days of differentiation


title: EBL.C.d7

value: 7 days of differentiation


title: GBM3565 5' CTCF boundary 4C-seq

tag: tissue

value: glioblastoma patient-derived cell model

tag: cell model id

value: amplified

value: DpnII, CviQI


title: dnFGFR_18hpf_4

value: new


title: Brain 5m WT Rep13

tag: genotype

value: WT

value: female


title: EBL.C.d6

value: 6 days of differentiation


title: EBL.C.d12

value: 12 days of differentiation


title: GSC23 TSS downstream 4C-seq

tag: egfr amplification status

value: unamplified

tag: cutting enzymes


title: dnFGFR_18hpf_5

tag: omit

value: FALSE

tag: method

tag: ko


title: dnFGFR_18hpf_3

tag: condition

tag: date


title: dnFGFR_20hpf_2


title: GBM3565 EGFR enhancer 2 4C-seq


title: Brain 5m WT Rep11

value: 5 months


title: Brain 5m WT Rep10


title: GSC23 TSS upstream 4C-seq


title: GSC23 EGFR enhancer 2 4C-seq


title: dnFGFR_18hpf_2

value: TRUE


title: GBM3565 EGFR enhancer 1 4C-seq


title: dnFGFR_18hpf_1

value: old


title: Brain 5m WT Rep9


title: EBL.C.d4

value: C


title: EBL.C.d5

value: Erythroid

value: 5 days of differentiation


title: Brain 5m WT Rep8


title: Brain 5m WT Rep7


title: EBL.C.d3

value: 3 days of differentiation


title: GBM3565 TSS upstream 4C-seq

value: glioblastoma patient-derived cell model


title: GBM3565 TSS downstream 4C-seq

value: amplified


title: EBL.C.d2

value: 2 days of differentiation


title: Brain 5m WT Rep6


title: dnFGFR_15hpf_1


title: EBL.C.d1

value: 1 days of differentiation


title: Brain 5m WT Rep5

value: WT


title: Bh_YL-15d-c

first: Run-Ze

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

institute: Chinese Academy of Sciences

description:
Bh_RP_15d-c
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 15 days, biological replicate 3.
processed data file: Gene expression and annotation.xlsx

data_processing:
RNA-seq: HISAT was used to perform genome mapping.
RNA-seq: StringTie v1.0.4 was used to reconstruct transcripts.
RNA-seq: Cuffcompare v2.2.1 was used to compare reconstructed transcripts to reference annotation.
RNA-seq: CPC v0.9-r2 was used to predict coding potential of novel transcripts.
RNA-seq: Bowtie2 v2.2.5 was used to map clean reads to reference.
Bisulfite-seq: BSMAP was used to map clean reads to reference with 2 forward strands.
Bisulfite-seq: Methylation level was determined by dividing the number of reads covering each mC by the total reads covering that cytosine, which was also equal the mC/C ratio at each reference cytosine.
Bisulfite-seq: Putative DMRs were identified by comparison of the sample1 and sample2 methylomes using windows that contained at least 5 CpG (CHG or CHH) sites with a 2-fold change in methylation level and Fisher test p value <= 0.05.
Genome_build: GCA_001598015.1 (Boea_hygrometrica.v1)
Supplementary_files_format_and_content: Gene expression and annotation.xlsx: Excel file includes FPKM values for each sample.
Supplementary_files_format_and_content: Differentially methylated region.xlsx: Excel file includes details of differentially methylated CG, CHG and CHH regions between samples.

organism: Dorcoceras hygrometricum

source_name: leaf explants

growth_protocol: Seeds of B. hygrometrica collected from wild plants growing in Beijing suburbs (China) were sterilized by immersion in 75% (v/v) ethanol solution for 1 min, followed by immersion in 10% (w/v) NaClO solution for 15 min and five times with sterile distilled water. Sterile seeds were vernalized at 4ºC in the dark for 3 days and then germinated on half-strength (1/2) MS medium supplemented with 1% sucrose and 0.6% agar under conditions of 16 h light/8 h dark at 25ºC for one week. No plant growth regulators (PGRs) were added. After germination, the seedlings were transferred to glass jars containing the same solid medium and continued to be cultured under the same environment condition.

extract_protocol:
The mixed samples of approximately 30 leaf discs in each biological replicate were used for RNA extraction followed by RNA-seq. Total RNA from leaf discs was isolated using RNAiso Plus (Takara) and further purified by DNase I (Promega) digestion. RNA integrity and concentration were analyzed using the Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) and the Agilent 2100 Bioanalyzer (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Young leaf samples excised from 1-month-old sterile parent plants were cut into segments (0.5 cm × 0.5 cm, length × breadth). These leaf discs were placed in Petri dishes containing 1/2 MS and the combinations of 2,4-D (0.1 mg/L) and 6-BA (0.1 mg/L). The excised leaves were cultured with the abaxial side in contact with the regeneration medium for 0, 5, 10 and 15 days.

value: leaf explants

tag: developmental stage

tag: treatment


title: Ngn_KO_10hpf_2

value: control

value: new


title: EBL.C.d0

tag: donor id

tag: cell type

value: 0 days of differentiation


title: Bh_YL-15d-b

description:
Bh_RP_15d-b
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 15 days, biological replicate 2.
processed data file: Gene expression and annotation.xlsx


title: Brain 5m WT Rep4

tag: age

tag: Sex

value: female


title: Bh_YL-15d-a

description:
Bh_RP_15d-a
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 15 days, biological replicate 1.
processed data file: Gene expression and annotation.xlsx


title: EBL.B.d12

value: B

tag: time

value: 12 days of differentiation


title: FoxF_KO_10hpf_3

tag: cell lineage

value: FALSE

value: TRUE


title: Brain 5m WT Rep3

value: 5 months


title: dnFGFR_15hpf_2

value: old


title: Brain 5m WT Rep2


title: Bh_YL-10d-c

description:
Bh_RP_10d-c
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 10 days, biological replicate 3.
processed data file: Gene expression and annotation.xlsx

tag: tissue


title: EBL.B.d9

value: Erythroid

value: 9 days of differentiation


title: Brain 5m WT Rep1

tag: genotype


title: FoxF_KO_10hpf_1


title: EBL.B.d6

value: 6 days of differentiation


title: Brain 4m WT Rep9

value: 4 months


title: Bh_YL-10d-b

description:
Bh_RP_10d-b
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 10 days, biological replicate 2.
processed data file: Gene expression and annotation.xlsx


title: FoxF_KO_10hpf_2


title: EBL.B.d7

value: 7 days of differentiation


title: Ngn_KO_10hpf_3


title: Bh_YL-10d-a

description:
Bh_RP_10d-a
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 10 days, biological replicate 1.
processed data file: Gene expression and annotation.xlsx


title: Bh_YL-5d-b

description:
Bh_RP_5d-b
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 5 days, biological replicate 2.
processed data file: Gene expression and annotation.xlsx

value: cultured in induction medium for 5 days


title: Bh_YL-5d-c

description:
Bh_RP_5d-c
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 5 days, biological replicate 3.
processed data file: Gene expression and annotation.xlsx

value: leaf explants


title: EBL.B.d5

value: 5 days of differentiation


title: MekMut_10hpf_3

value: new


title: Ngn_KO_10hpf_1

value: control


title: MekMut_10hpf_1


title: MekMut_10hpf_2


title: Brain 4m WT Rep7

value: WT

value: female


title: Bh_YL-0d-b

description:
Bh_RP_0d-b
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 0 day, biological replicate 2.
processed data file: Gene expression and annotation.xlsx

value: cultured in induction medium for 0 day


title: Bh_YL-5d-a

description:
Bh_RP_5d-a
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 5 days, biological replicate 1.
processed data file: Gene expression and annotation.xlsx


title: dnFGFR_10hpf_3

value: FALSE


title: dnFGFR_10hpf_2


title: EBL.B.d1

value: B

value: 1 days of differentiation


title: Brain 4m WT Rep4


title: Brain 4m WT Rep6


title: EBL.B.d3

value: 3 days of differentiation


title: Bh_YL-0d-a

description:
Bh_RP_0d-a
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 0 day, biological replicate 1.
processed data file: Gene expression and annotation.xlsx


title: EBL.B.d0

value: Erythroid

value: 0 days of differentiation


title: Brain 4m WT Rep3


title: EBL.A.d12

value: A

value: 12 days of differentiation


title: Bh_YL-0d-c

description:
Bh_RP_0d-c
Young leaf explants of 1-month-old Boea hygrometrica cultured in induction medium for 0 day, biological replicate 3.
processed data file: Gene expression and annotation.xlsx


title: Brain 4m WT Rep5

value: 4 months


title: EBL.A.d9

value: 9 days of differentiation


title: EBL.B.d2

value: 2 days of differentiation


title: LacZ_10hpf_3


title: ALE-3 Replicate_2

city: San Diego

first: Amitesh

last: Anand

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-Seq were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package with strand inversion for the dUTP protocol and strict intersection mode
Estimated the dispersion of each gene using DESeq2
Transcript per Million (TPM) were calculated by DESeq2
Genome_build: E.coli genome(NC_000913.3)
Supplementary_files_format_and_content: csv file includes TPM values for each Sample

organism: Escherichia coli K-12

source_name: bacteria

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with glucose as carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol: KAPA Stranded RNA-Seq Kit

tag: strain

tag: media

value: M9 minimal media w/ 4g/L glucose


title: Brain 4m WT Rep1


title: Brain 4m WT Rep8


title: dnFGFR_10hpf_1

tag: omit

value: new


title: EBL.A.d6

value: 6 days of differentiation


title: Brain 2m WT Rep4

value: 2 months

value: WT


title: Brain 2m WT Rep3

value: female


title: LacZ_10hpf_1

value: control

value: FALSE

tag: method


title: ∆pdhR Replicate_2

value: {delta}pdhR


title: LacZ_10hpf_4

tag: ko


title: LacZ_6hpf_2

source_name: FC

tag: condition


title: LacZ_6hpf_3

tag: date


title: EBL.B.d4

value: B

value: 4 days of differentiation


title: ALE-2 Replicate_2


title: ∆pdhR Replicate_1


title: Brain 4m WT Rep2


title: ALE-1 Replicate_1


title: LacZ_6hpf_1


title: Psojae_suz12_KO_MY_RNA-seq_rep2

city: Nanjing

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

data_processing:
Clean reads were aligned to Psojae v1.1 whole genome using hisat2 v2.1.0 with default parameters
FPKM were calculated using stringtie v1.3.3b with default parameters
Genome_build: Psojae v1.1
Supplementary_files_format_and_content: gtf files include FPKM,TPM,and coverage values for each Sample …

organism: Phytophthora sojae

source_name: mycelium

growth_protocol: V8 medium

extract_protocol:
RNA were extracted using OMEGA total RNA Kit I (Cat.#:R6834-04)
Library followed the standard Illumina protocol

value: mycelium


title: naked mole-rat whole spleen LPS-challenged replicate 2

city: South San Francisco

first: Nimrod

middle: Daniel

last: Rubinstein

address: 1170 Veterans blvd

institute: Calico

data_processing:
Single-cell fastq files were demultiplexed to their respective barcodes using the 10X Genomics Cell Ranger mkfastq utility
Unique Molecular Identifier (UMI) counts were generated for each barcode using the Cell Ranger count utility using the mm10 reference genome and the mouse Gencode version M12 annotation  for mouse and HetGla2.0 reference genome along with the RefSeq GCF_000247695.1 annotation for naked mole-rat
For each single-cell sample barcodes that were not likely to represent captured cells were filtered out by detecting the first local minimum above 2 in a distribution of log10(#UMIs).
For each single-cell sample genes that are too sparsely captured across barcodes were filtered out by detecting the first local minimum above 3 in a distribution of log10(#barcodes)
For each single-cell sample barcodes capturing more than a single cell (multiplets) were sought as local modes in the distributions of log10(#genes) and log10(#UMIs), whose x-axis maxima are more than 1.5 higher than that of the x-axis location of the global maximum of the respective distribution and includes less than 5% of the total number of barcodes
Whole spleen RNA read data were mapped using STAR aligner version 2.5.3a
Transcript and gene abundances of whole spleen mapped RNA read data were quantified using MMSEQ
Genome_build: For mouse: mm10 reference genome and the mouse Gencode version M12 annotation. For naked mole-rat the HetGla2.0 reference genome and the RefSeq GCF_000247695.1 annotation for naked mole-rat
Supplementary_files_format_and_content: For the single-cell data processed data files are comma separated matrices of UMI counts where rows are gene IDs (Ensembl for mouse and Entrez for naked mole-rat) and columns are barcodes. The genes and barcode that are included are those that were retained following all filtering steps

organism: Heterocephalus glaber

source_name: whole spleen

extract_protocol:
1ml TRIzol reagent (4C) (Invitrogen, 15596026) added to 20mg frozen splenic tissue in a 2ml microcentrifuge tube along with a single stainless-steel bead (Qiagen, 69965) and homogenization was performed using a Tissuelyser II (Qiagen) (30Hz for 2mins)
Illumina TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit
Single cells were extracted using 10X Genomics Chromium Controller droplet emulsion capture. Whole tissue RNA was purified using 1ml TRIzol reagent (4C) (Invitrogen, 15596026) added to 20mg frozen splenic tissue in a 2ml microcentrifuge tube along with a single stainless-steel bead (Qiagen, 69965) and homogenization was performed using a Tissuelyser II (Qiagen) (30Hz for 2mins)
Single cell libraries were contructed using 10X Genomics Chromium Single-Cell 3’ Gel Bead and Library V2 Kit, suspending cells in PBS with 5% FBS to a final concentration of 1 x 10^6 cells/ml (1000 cells per ul) and loaded in each channel with a target output of 3000 cells. Reactions performed with Bio-Rad C100 Touch Thermal Cycler with a 96 Deep Well Reaction Module, 12 cycles for cDNA amplificationand OCR indexing. Whole spleen RNA libraries were contructed using Illumina TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit

treatment_protocol: all animals were anasthesiasized with isoflurane. Saline controls received an intraperitoneal 200µl sterile saline injection. LPS-chllaneged animals received an intraperitoneal 1mg/kg lipopolysaccharide injection

value: whole spleen

value: LPS challenge

value: 23-25 months old


title: ∆ubiC Replicate_2

value: {delta}ubiC


title: EBL.A.d1

value: A

value: Erythroid

value: 1 days of differentiation


title: ∆ubiC Replicate_1

value: M9 minimal media w/ 4g/L glucose


title: WT Replicate_1


title: EBL.A.d7

value: 7 days of differentiation


title: ALE-3 Replicate_1


title: Brain 2m WT Rep5

value: 2 months

value: WT


title: naked mole-rat circulating immune cells LPS-challenged sample 2 replicate 1

source_name: single circulating immune cells

extract_protocol:
10X Genomics Chromium Controller droplet emulsion capture
10X Genomics Chromium Single-Cell 3’ Gel Bead and Library V2 Kit, suspending cells in PBS with 5% FBS to a final concentration of 1 x 10^6 cells/ml (1000 cells per ul) and loaded in each channel with a target output of 3000 cells. Reactions performed with Bio-Rad C100 Touch Thermal Cycler with a 96 Deep Well Reaction Module, 12 cycles for cDNA amplificationand OCR indexing
Single cells were extracted using 10X Genomics Chromium Controller droplet emulsion capture. Whole tissue RNA was purified using 1ml TRIzol reagent (4C) (Invitrogen, 15596026) added to 20mg frozen splenic tissue in a 2ml microcentrifuge tube along with a single stainless-steel bead (Qiagen, 69965) and homogenization was performed using a Tissuelyser II (Qiagen) (30Hz for 2mins)
Single cell libraries were contructed using 10X Genomics Chromium Single-Cell 3’ Gel Bead and Library V2 Kit, suspending cells in PBS with 5% FBS to a final concentration of 1 x 10^6 cells/ml (1000 cells per ul) and loaded in each channel with a target output of 3000 cells. Reactions performed with Bio-Rad C100 Touch Thermal Cycler with a 96 Deep Well Reaction Module, 12 cycles for cDNA amplificationand OCR indexing. Whole spleen RNA libraries were contructed using Illumina TruSeq Stranded Total RNA kit paired with the Ribo-Zero rRNA removal kit

value: single circulating immune cells

value: female


title: LacZ_10hpf_2

value: control

value: FALSE

value: new


title: EBL.A.d5

value: 5 days of differentiation


title: ALE-2 Replicate_1


title: Psojae_suz12_KO_MY_input_rep1

data_processing:
Clean reads were aligned to Psojae v1.1 and Pinfestans whole genome using bowtie2 v2.3.3.1 with parameter -N 1
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None
Genome_build: Psojae v1.1
Supplementary_files_format_and_content: Bigwig files, scores represent enriched value(log2(fold-change))

extract_protocol:
After antibody Immunoprecipitation, target DNA was eluted from Dynabeads and precipitated using ethanol followed by twice washes, finally the samples was dried and dissolved in 33 μl ddH2O
Qualified library for sequencing was prepared using the QIAquick PCR Purification Kit(Qiagen). Briefly, 10-300ng DNA was taken to do DNA-end repair(3'-dA overhang and ligation of methylated sequencing adaptors) followed by PCR amplication and size selection (usually 100-300bp, including adaptor sequencing).

value: mycelium

tag: chip antibody


title: naked mole-rat circulating immune cells LPS-challenged sample 1 replicate 2

value: LPS challenge

value: male


title: EBL.A.d4

value: 4 days of differentiation


title: Brain 2m WT Rep2


title: ALE-1 Replicate_2


title: Ecoli_rne(ΔMTS)_T7_kinetic3

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

institute: TBI

description:
Escherichia coli MG1677
Cells were in mid-exponential phase, the sampling was performed 7 minutes after rifampicin addition. It is the third kinetics out of 3 for this strain.

hyb_protocol: According to manufacturer instructions, 2 µg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) during 17 h at 42 °C.

scan_protocol: Arrays were later washed and scanned using MS200 Microarray Scanner (Nimblegen, Roche). Pictures were analyzed with DEVA 1.2.1 software.

data_processing:
Raw probe intensities ( .pair files three replicates for each strain before and after transcription arrest by rifampicin addition) were processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Twelve arrays (three reference T0 samples, and nine time points after addition of rifampicin) were used. Only a normalization between arrays according to an invariant probeset intensities was performed. For each strain, a set of probes in the background for which the ranks were roughly invariant across all twelve arrays was selected. The median value of the invariant probe set intensities in each condition was used as a scaling factor for normalization between the three strains. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure [Irizarry et al, 2003, Biostatistics 4(2): 249-264] within each condition.
After normalization, in each array, transcript-specific intensity was computed as the median value of the 16 targeting probe intensities.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli, rne(ΔMTS), Sampling 7 minutes after rifampicin addition in kinetic 3

label_protocol: According to manufacturer instructions, 1 µg of cDNA was labeled using one color DNA labeling kit.

growth_protocol: The laboratory strain E. coli K12 MG1655 referred as the rne+ strain and its mutant strain E. coli rne (ΔMTS) were grown in bioreactors in M9 glucose (3g/l) at 37 °C. The pH was set to 7. All cultures were inoculated at OD 0.1 from overnight pre-cultures performed in similar conditions. Biomass was estimated from absorbance at 600 nm. Each culture was repeated three times to provide independent biological kinetics.

extract_protocol: After thawing and centrifugation steps, total RNA was extracted with TRIZOL® Reagent (Ambion) according to the manufacturer’s instructions. DNA contamination was eliminated with Turbo DNase kit (Ambion). Total RNA concentration and integrity were measured using a Nanodrop® spectrophotometer and Agilent BioAnalyzer, respectively.

treatment_protocol: In mid-exponential phase, samples were collected for the reference time point (T0) for the half-life determination procedure. Subsequently, rifampicin (500 µg.mL-1) was added to inhibit the initiation of transcription, and cells were harvested at three different time points after this addition. Cultures were performed in triplicate. Samples were immediately frozen in liquid nitrogen upon collection.

tag: genotype/variation

value: rne(deltaMTS)

tag: treatment

value: rifampicin

tag: sampling time

value: 7 minutes after rifampicin addition

tag: repetition

value: kinetic 3


title: EBL.A.d3

tag: donor id

value: A

tag: cell type

value: Erythroid

value: 3 days of differentiation


title: EBL.A.d2

tag: time

value: 2 days of differentiation


title: naked mole-rat circulating immune cells saline control sample 2 replicate 2

tag: tissue

value: single circulating immune cells

value: saline control

tag: Sex

value: female

tag: age

value: 23-25 months old


title: naked mole-rat whole spleen LPS-challenged replicate 1

value: whole spleen


title: Ecoli_rne(ΔMTS)_T0_kinetic3

description:
Escherichia coli MG1675
Cells were in mid-exponential phase, the sampling was performed just before rifampicin addition. It is the third kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling before rifampicin addition in kinetic 3

value: before rifampicin addition


title: Psojae_WT_MY_input_rep2

tag: strain

value: mycelium


title: Psojae_suz12_KO_MY_H3K27me3_rep3


title: EBL.A.d0

value: 0 days of differentiation


title: naked mole-rat circulating immune cells saline control sample 2 replicate 1


title: Psojae_suz12_KO_MY_RNA-seq_rep1


title: naked mole-rat whole spleen saline control replicate 2

value: male


title: Psojae_WT_MY_input_rep1


title: WT Replicate_2

tag: media

value: M9 minimal media w/ 4g/L glucose

tag: genotype

value: WT


title: naked mole-rat whole spleen saline control replicate 1


title: Psojae_suz12_KO_MY_H3K27me3_rep1


title: Ecoli_rne(ΔMTS)_T5_kinetic2

description:
Escherichia coli MG1673
Cells were in mid-exponential phase, the sampling was performed 5 minutes after rifampicin addition. It is the second kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling 5 minutes after rifampicin addition in kinetic 2

value: rne(deltaMTS)

value: rifampicin

value: 5 minutes after rifampicin addition

value: kinetic 2


title: Psojae_suz12_KO_MY_input_rep2


title: Ecoli_rne(ΔMTS)_T0_kinetic2

description:
Escherichia coli MG1671
Cells were in mid-exponential phase, the sampling was performed just before rifampicin addition. It is the second kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling before rifampicin addition in kinetic 2


title: Ecoli_rne(ΔMTS)_T11_kinetic3

description:
Escherichia coli MG1678
Cells were in mid-exponential phase, the sampling was performed 11 minutes after rifampicin addition. It is the third kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling 11 minutes after rifampicin addition in kinetic 3

value: 11 minutes after rifampicin addition

value: kinetic 3


title: naked mole-rat spleen LPS-challenged sample 2 replicate 2

source_name: single spleen cells

value: single spleen cells

value: LPS challenge


title: Ecoli_rne(ΔMTS)_T11_kinetic2

description:
Escherichia coli MG1674
Cells were in mid-exponential phase, the sampling was performed 11 minutes after rifampicin addition. It is the second kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling 11 minutes after rifampicin addition in kinetic 2


title: naked mole-rat spleen LPS-challenged sample 2 replicate 1

value: female


title: LO3

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
After importing of FASTQ files, raw sequencing reads were trimmed based on quality score (Q-score >20 was considered high-quality data), removal of adaptor sequences and discarding reads with length <15 bp.
Sequence reads were mapped and annotated to the Sus scrofa reference genome with genes and transcripts
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization)
Expression analysis has been done using Differential Expression In Two Groups tool of CLC Genomics Workbench v. 12.0 based on a negative binomial Generalized Linear Model (GLM) function.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: A matrix table including total read count and Tags Per Million (TPM) values for each sample with gene ID.

organism: Sus scrofa

source_name: Oocyte

extract_protocol:
Total RNA was isolated from denuded oocytes of the two different groups (three replicates each, n= 360) using an AllPrep DNA/RNA Micro Kit (Qiagen) according to the manufacturer’s instructions.
The RNA libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Porcine ovaries were collected from prepubertal gilts at a local abattoir and transported to our laboratory in flask within 3 h after slaughter. Ovaries were washed three times with saline solution. COCs were aspirated from small follicles with diameter 1.5-1.9 mm (SO) using a 23-gauge needle attached to a 5 mL syringe or from large follicles with diameter from 3 to 6 mm (LO) using 20-gauge needle attached to a 10 mL syringe.

value: Prepubertal gilts

tag: size

value: Large (3-6 mm)


title: SO2


title: LO2


title: Psojae_suz12_KO_MY_H3K27me3_rep2


title: naked mole-rat spleen LPS-challenged sample 1 replicate 1

tag: condition

value: 23-25 months old


title: Ecoli_rne(ΔMTS)_T4_kinetic1

description:
Escherichia coli MG1669
Cells were in mid-exponential phase, the sampling was performed 4 minutes after rifampicin addition. It is the first kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling 4 minutes after rifampicin addition in kinetic 1

value: 4 minutes after rifampicin addition

value: kinetic 1


title: Psojae_WT_MY_H3K27me3_rep2

value: mycelium


title: naked mole-rat circulating immune cells LPS-challenged sample 2 replicate 2

value: single circulating immune cells


title: LO1


title: naked mole-rat circulating immune cells LPS-challenged sample 1 replicate 1

value: male


title: Ecoli_rne(ΔMTS)_T3_kinetic3

description:
Escherichia coli MG1676
Cells were in mid-exponential phase, the sampling was performed 3 minutes after rifampicin addition. It is the third kinetics out of 3 for this strain.

source_name: E. coli, rne(ΔMTS), Sampling 3 minutes after rifampicin addition in kinetic 3

value: rne(deltaMTS)

value: 3 minutes after rifampicin addition